Museomics

Today's natural history museums are true treasure troves, not only for curious visitors,
but also for molecular biologists. Many of the samples used for our projects come from
museum collections and are associated with a wealth of additional information that was
recorded at the time of collection. An invaluable source of information are the museum
curators, who like to know the molecular-genetic characteristics of a given specimen.
Since many of these are
type specimens,
which define a given species, it is of great interest to attach the DNA sequence for a
given fossil or other specimen in order to facilitate the molecular-genetic classification
and analysis of modern samples.

A large number of collections stored in natural history museums are now within reach of
molecular genomic analysis. Our proposed analyses of type specimens might therefore open
the door to an area we call "museomics" -- the large-scale analysis of the DNA
content of museum collections.

Examples of the Scientific Questions to be Addressed

Genetic diversity as related to mammalian extinctions.
A major goal is to learn how genetic diversity changes (if at all) as a
species approaches extinction, which may well assist with conservation plans
for endangered species. One approach would be to sample large percentages of
global museum holdings for all recently extinct mammals for which adequate
numbers of individuals across a reasonable timeframe (multiple decades at
least) are available. (Note that approaching diversity through time with
museum collections is especially powerful because samples are usually dated
to the nearest year, and commonly to the exact date and month.) Species
meeting these criteria include approximately five Australian marsupials,
the Caribbean monk seal, Japanese sea lion, perhaps Steller's sea cow, two
bat species, possibly the Falkland Islands wolf, and a handful of rodents.
Pre-extinction patterns of diversity can be compared across unrelated mammals
that have suffered global extinction. For example, is there any overwhelming
shared signature of mtDNA diversity that precedes global extinction in a
predictable manner across taxa? Or is this different for every species based
on the unique conditions of its particular decline?

Documenting the spread of disease from invasive to native species.
Dates of local (e.g. insular) or global extinction are known for many mammal
species and populations with reasonable accuracy, as are dates of exotic
introduction/invasion of certain species into novel landscapes. In some cases
it is suspected that extinctions of native species have followed causally from
introductions of certain invasive species (especially on islands) and that
disease may be involved in some of these cases, but these types of claims
generally remain anecdotal. The timing of the global decline of certain endemic
insular rodent (and potentially other small mammal) lineages and the global
spread of commensal rats offer many iterative, analogous cases for studying
the spread of disease from invasive rats (with enormous global population sizes
and greater exposure to a vast array of pathogens across time and geography)
to comparatively "naive" and isolated endemic rodents with much smaller
population sizes and less extensive historical exposure to disease. We predict
that comparisons of metagenomes/bacteriomes/viromes sequenced from museum hair
samples will be illuminating here.

What next?

A systematic study is needed to determine factors affecting the utility of
museum specimens for molecular analysis. In our case, did analysis of one
Smithsonian sample fail and another prove very successful (see the
online supplement for our recent paper) because
of differences in exposure to light over a long period? Experiments using
comparatively expendable museum specimens with varying documented histories
of preservation, storage, etc., are needed to inform museum personnel which
sampling risks are more likely to pay off than others, and also how best to
preserve both existing and newly acquired specimens for future molecular
analysis. One component of such studies will be to determine which
associations with microbial species result from particular preservation
and/or storage histories, and which reflect the microbiome of the living
animal. These studies, together with an inventory of global museum holdings,
will set the stage for coordinated and appropriate use of museum specimens
to deepen our understanding of evolution and the extinction process.